[HTML][HTML] Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
In this paper we report the improvements and extensions of the UNRES server (https://unres-
server. chem. ug. edu. pl) for physics-based simulations with the coarse-grained UNRES …
server. chem. ug. edu. pl) for physics-based simulations with the coarse-grained UNRES …
[HTML][HTML] Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
KM Ocetkiewicz, C Czaplewski, H Krawczyk… - Computer Physics …, 2024 - Elsevier
Abstract Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular
simulations because of the advantage of efficient partitioning of atom pairs between the …
simulations because of the advantage of efficient partitioning of atom pairs between the …
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
C Czaplewski, A Karczyńska… - Nucleic Acids …, 2018 - academic.oup.com
A server implementation of the UNRES package (http://www. unres. pl) for coarse-grained
simulations of protein structures with the physics-based UNRES model, coined a name …
simulations of protein structures with the physics-based UNRES model, coined a name …
UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time-and size-scales
KM Ocetkiewicz, C Czaplewski, H Krawczyk… - …, 2023 - academic.oup.com
Abstract Summary The UNited RESisdue (UNRES) package for coarse-grained simulations,
which has recently been optimized to treat large protein systems, has been implemented on …
which has recently been optimized to treat large protein systems, has been implemented on …
Extension of the Unres package for physics-based coarse-grained simulations of proteins and protein complexes to very large systems
Tuesday, February 23, 2021 83a analytical expressions for the energy terms [3]. Owing to
such rigorous derivation, UNRES is capable of reliable modeling of protein structure and …
such rigorous derivation, UNRES is capable of reliable modeling of protein structure and …
Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone-and side-chain-local conformational states
The UNited RESidue (UNRES) coarse-grained model of polypeptide chains, developed in
our laboratory, enables us to carry out millisecond-scale molecular-dynamics simulations of …
our laboratory, enables us to carry out millisecond-scale molecular-dynamics simulations of …
Use of restraints from consensus fragments of multiple server models to enhance protein-structure prediction capability of the UNRES force field
MA Mozolewska, P Krupa, B Zaborowski… - Journal of Chemical …, 2016 - ACS Publications
Recently, we developed a new approach to protein-structure prediction, which combines
template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) …
template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) …
An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and …
H Shen, A Liwo, HA Scheraga - The Journal of Physical Chemistry …, 2009 - ACS Publications
Coarse-grained or mesoscopic models of proteins and the corresponding force fields are of
great importance because they enable us to reduce the folding simulation time by several …
great importance because they enable us to reduce the folding simulation time by several …
Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of …
A Liwo, C Czaplewski - The Journal of chemical physics, 2020 - pubs.aip.org
The force-matching approach to coarse graining, in which the forces that act on site centers
are fitted to the respective average forces computed from all-atom molecular dynamics …
are fitted to the respective average forces computed from all-atom molecular dynamics …
Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
AK Sieradzan, J Sans‐Duñó… - Journal of …, 2023 - Wiley Online Library
We report major algorithmic improvements of the UNRES package for physics‐based coarse‐
grained simulations of proteins. These include (i) introduction of interaction lists to optimize …
grained simulations of proteins. These include (i) introduction of interaction lists to optimize …